@jbrowse/plugin-sequence 2.10.2 → 2.10.3

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Files changed (9) hide show
  1. package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts +2 -0
  2. package/dist/DivSequenceRenderer/components/DivSequenceRendering.js +17 -13
  3. package/dist/LinearReferenceSequenceDisplay/model.d.ts +38 -19
  4. package/dist/LinearReferenceSequenceDisplay/model.js +24 -8
  5. package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +2 -0
  6. package/esm/DivSequenceRenderer/components/DivSequenceRendering.js +17 -13
  7. package/esm/LinearReferenceSequenceDisplay/model.d.ts +38 -19
  8. package/esm/LinearReferenceSequenceDisplay/model.js +24 -8
  9. package/package.json +2 -2
package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -9,6 +9,8 @@ declare const DivSequenceRendering: (props: {
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  features: Map<string, Feature>;
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  regions: Region[];
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  bpPerPx: number;
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+ rowHeight: number;
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+ sequenceHeight: number;
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  config: AnyConfigurationModel;
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  theme?: Theme;
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  showForward?: boolean;
package/dist/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -41,7 +41,7 @@ function Translation(props) {
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  : util_1.defaultStops.includes(codon)
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  ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
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  : map[Math.abs(frame)] }),
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- render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
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+ render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2 }, letter)) : null));
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  })));
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  }
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  function DNA(props) {
@@ -57,14 +57,13 @@ function DNA(props) {
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  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
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  return (react_1.default.createElement(react_1.default.Fragment, { key: index },
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  react_1.default.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
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- render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
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+ render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
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  })));
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  }
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- function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) {
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+ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, rowHeight, }) {
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  const [region] = regions;
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  const theme = (0, ui_1.createJBrowseTheme)(configTheme);
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  const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
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- const height = 20;
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  const [feature] = [...features.values()];
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  if (!feature) {
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  return null;
@@ -75,26 +74,31 @@ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showRe
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  }
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  // incrementer for the y-position of the current sequence being rendered
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  // (applies to both translation rows and dna rows)
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- let currY = -20;
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+ let currY = -rowHeight;
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  return (react_1.default.createElement(react_1.default.Fragment, null,
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  showTranslation && (region.reversed ? showReverse : showForward)
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- ? [2, 1, 0].map(index => (react_1.default.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: region.reversed })))
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+ ? [2, 1, 0].map(index => (react_1.default.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: rowHeight, reverse: region.reversed })))
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  : null,
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- showForward ? (react_1.default.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
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- showReverse ? (react_1.default.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null,
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+ showForward ? (react_1.default.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
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+ showReverse ? (react_1.default.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null,
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  showTranslation && (region.reversed ? showForward : showReverse)
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- ? [0, -1, -2].map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
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+ ? [0, -1, -2].map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: rowHeight, reverse: !region.reversed })))
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  : null));
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  }
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  function Wrapper({ exportSVG, width, totalHeight, children, }) {
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- return exportSVG ? (react_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight, userSelect: 'none' } }, children));
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+ return exportSVG ? (react_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
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+ width,
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+ height: totalHeight,
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+ userSelect: 'none',
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+ // use block because svg by default is inline, which adds a margin
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+ display: 'block',
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+ } }, children));
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  }
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  const DivSequenceRendering = (0, mobx_react_1.observer)(function (props) {
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- const { regions, bpPerPx } = props;
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+ const { regions, bpPerPx, sequenceHeight } = props;
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  const [region] = regions;
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  const width = (region.end - region.start) / bpPerPx;
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- const totalHeight = 200;
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- return (react_1.default.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
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+ return (react_1.default.createElement(Wrapper, { ...props, totalHeight: sequenceHeight, width: width },
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  react_1.default.createElement(SequenceSVG, { ...props })));
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  });
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  exports.default = DivSequenceRendering;
package/dist/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -31,9 +31,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  }, {
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  renderInProgress: AbortController | undefined;
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- /**
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- * #method
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- */
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  filled: boolean;
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  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -43,8 +40,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
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- model: any;
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- }) => any;
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+ model: {
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+ error?: unknown;
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+ reload: () => void;
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+ message: import("react").ReactNode;
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+ filled?: boolean | undefined;
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+ status?: string | undefined;
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+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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+ };
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+ }) => import("react").JSX.Element | undefined;
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  renderProps: any;
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  } & {
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  doReload(): void;
@@ -77,7 +81,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  height: {
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  type: string;
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  defaultValue: number;
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- description: string;
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+ description: string; /**
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+ * #property
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+ */
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  };
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  mouseover: {
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  type: string;
@@ -122,9 +128,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
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  model: {
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- id: string; /**
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- * #action
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- */
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+ id: string;
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  type: string;
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  rpcDriverName: string | undefined;
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -141,9 +145,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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  }> | null;
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- /**
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- * #method
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- */
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  readonly adapterConfig: any;
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  readonly parentTrack: any;
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  renderProps(): any;
@@ -178,7 +179,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  readonly featureDensityStatsReady: boolean;
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  readonly maxAllowableBytes: number;
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  } & {
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- afterAttach(): void;
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+ afterAttach(): void; /**
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+ * #getter
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+ */
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  } & {
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  setCurrStatsBpPerPx(n: number): void;
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  setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
@@ -225,6 +228,16 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  } & {
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  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
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  afterAttach(): void;
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+ } & {
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+ /**
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+ * #property
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+ */
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+ rowHeight: number;
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+ } & {
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+ /**
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+ * #getter
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+ */
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+ readonly sequenceHeight: number;
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  } & {
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  /**
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  * #method
@@ -292,9 +305,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  }, {
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  renderInProgress: AbortController | undefined;
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- /**
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- * #method
297
- */
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  filled: boolean;
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  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -304,8 +314,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
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- model: any;
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- }) => any;
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+ model: {
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+ error?: unknown;
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+ reload: () => void;
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+ message: import("react").ReactNode;
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+ filled?: boolean | undefined;
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+ status?: string | undefined;
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+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
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+ };
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+ }) => import("react").JSX.Element | undefined;
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  renderProps: any;
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  } & {
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  doReload(): void;
@@ -338,7 +355,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  height: {
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  type: string;
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  defaultValue: number;
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- description: string;
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+ description: string; /**
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+ * #property
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+ */
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  };
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  mouseover: {
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  type: string;
package/dist/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -33,6 +33,26 @@ function modelFactory(configSchema) {
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  * #property
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  */
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  showTranslation: true,
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+ }))
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+ .volatile(() => ({
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+ /**
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+ * #property
40
+ */
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+ rowHeight: 15,
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+ }))
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+ .views(self => ({
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+ /**
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+ * #getter
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+ */
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+ get sequenceHeight() {
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+ const { showTranslation, showReverse, showForward } = self;
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+ const r1 = showReverse && showTranslation ? self.rowHeight * 3 : 0;
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+ const r2 = showForward && showTranslation ? self.rowHeight * 3 : 0;
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+ const t = r1 + r2;
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+ const r = showReverse ? self.rowHeight : 0;
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+ const s = showForward ? self.rowHeight : 0;
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+ return t + r + s;
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+ },
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  }))
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  .views(self => {
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  const { renderProps: superRenderProps } = self;
@@ -41,7 +61,7 @@ function modelFactory(configSchema) {
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  * #method
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  */
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  renderProps() {
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- const { showForward, rpcDriverName, showReverse, showTranslation } = self;
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+ const { showForward, rpcDriverName, showReverse, showTranslation, rowHeight, sequenceHeight, } = self;
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  return {
46
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  ...superRenderProps(),
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  config: self.configuration.renderer,
@@ -49,6 +69,8 @@ function modelFactory(configSchema) {
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  showForward,
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  showReverse,
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  showTranslation,
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+ rowHeight,
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+ sequenceHeight,
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  };
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  },
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  };
@@ -94,13 +116,7 @@ function modelFactory(configSchema) {
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  self.setHeight(50);
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  }
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  else {
97
- const { showTranslation, showReverse, showForward } = self;
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- const r1 = showReverse && showTranslation ? 60 : 0;
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- const r2 = showForward && showTranslation ? 60 : 0;
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- const t = r1 + r2;
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- const r = showReverse ? 20 : 0;
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- const s = showForward ? 20 : 0;
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- self.setHeight(t + r + s);
119
+ self.setHeight(self.sequenceHeight);
104
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  }
105
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  }));
106
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  },
package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -9,6 +9,8 @@ declare const DivSequenceRendering: (props: {
9
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  features: Map<string, Feature>;
10
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  regions: Region[];
11
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  bpPerPx: number;
12
+ rowHeight: number;
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+ sequenceHeight: number;
12
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  config: AnyConfigurationModel;
13
15
  theme?: Theme;
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  showForward?: boolean;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -36,7 +36,7 @@ function Translation(props) {
36
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  : defaultStops.includes(codon)
37
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  ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
38
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  : map[Math.abs(frame)] }),
39
- render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
39
+ render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2 }, letter)) : null));
40
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  })));
41
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  }
42
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  function DNA(props) {
@@ -52,14 +52,13 @@ function DNA(props) {
52
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  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
53
53
  return (React.createElement(React.Fragment, { key: index },
54
54
  React.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
55
- render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
55
+ render ? (React.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black' }, letter)) : null));
56
56
  })));
57
57
  }
58
- function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, }) {
58
+ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showReverse = true, showForward = true, showTranslation = true, bpPerPx, rowHeight, }) {
59
59
  const [region] = regions;
60
60
  const theme = createJBrowseTheme(configTheme);
61
61
  const codonTable = generateCodonTable(defaultCodonTable);
62
- const height = 20;
63
62
  const [feature] = [...features.values()];
64
63
  if (!feature) {
65
64
  return null;
@@ -70,26 +69,31 @@ function SequenceSVG({ regions, theme: configTheme, features = new Map(), showRe
70
69
  }
71
70
  // incrementer for the y-position of the current sequence being rendered
72
71
  // (applies to both translation rows and dna rows)
73
- let currY = -20;
72
+ let currY = -rowHeight;
74
73
  return (React.createElement(React.Fragment, null,
75
74
  showTranslation && (region.reversed ? showReverse : showForward)
76
- ? [2, 1, 0].map(index => (React.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: region.reversed })))
75
+ ? [2, 1, 0].map(index => (React.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: rowHeight, reverse: region.reversed })))
77
76
  : null,
78
- showForward ? (React.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
79
- showReverse ? (React.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
77
+ showForward ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
78
+ showReverse ? (React.createElement(DNA, { height: rowHeight, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null,
80
79
  showTranslation && (region.reversed ? showForward : showReverse)
81
- ? [0, -1, -2].map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
80
+ ? [0, -1, -2].map(index => (React.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: rowHeight, reverse: !region.reversed })))
82
81
  : null));
83
82
  }
84
83
  function Wrapper({ exportSVG, width, totalHeight, children, }) {
85
- return exportSVG ? (React.createElement(React.Fragment, null, children)) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight, userSelect: 'none' } }, children));
84
+ return exportSVG ? (React.createElement(React.Fragment, null, children)) : (React.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
85
+ width,
86
+ height: totalHeight,
87
+ userSelect: 'none',
88
+ // use block because svg by default is inline, which adds a margin
89
+ display: 'block',
90
+ } }, children));
86
91
  }
87
92
  const DivSequenceRendering = observer(function (props) {
88
- const { regions, bpPerPx } = props;
93
+ const { regions, bpPerPx, sequenceHeight } = props;
89
94
  const [region] = regions;
90
95
  const width = (region.end - region.start) / bpPerPx;
91
- const totalHeight = 200;
92
- return (React.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
96
+ return (React.createElement(Wrapper, { ...props, totalHeight: sequenceHeight, width: width },
93
97
  React.createElement(SequenceSVG, { ...props })));
94
98
  });
95
99
  export default DivSequenceRendering;
package/esm/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -31,9 +31,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
31
31
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
32
32
  }, {
33
33
  renderInProgress: AbortController | undefined;
34
- /**
35
- * #method
36
- */
37
34
  filled: boolean;
38
35
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
39
36
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -43,8 +40,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
43
40
  message: string | undefined;
44
41
  maxHeightReached: boolean;
45
42
  ReactComponent: ({ model, }: {
46
- model: any;
47
- }) => any;
43
+ model: {
44
+ error?: unknown;
45
+ reload: () => void;
46
+ message: import("react").ReactNode;
47
+ filled?: boolean | undefined;
48
+ status?: string | undefined;
49
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
50
+ };
51
+ }) => import("react").JSX.Element | undefined;
48
52
  renderProps: any;
49
53
  } & {
50
54
  doReload(): void;
@@ -77,7 +81,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
77
81
  height: {
78
82
  type: string;
79
83
  defaultValue: number;
80
- description: string;
84
+ description: string; /**
85
+ * #property
86
+ */
81
87
  };
82
88
  mouseover: {
83
89
  type: string;
@@ -122,9 +128,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
122
128
  }>;
123
129
  readonly DisplayBlurb: import("react").FC<{
124
130
  model: {
125
- id: string; /**
126
- * #action
127
- */
131
+ id: string;
128
132
  type: string;
129
133
  rpcDriverName: string | undefined;
130
134
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -141,9 +145,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
141
145
  message: string | undefined;
142
146
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
143
147
  }> | null;
144
- /**
145
- * #method
146
- */
147
148
  readonly adapterConfig: any;
148
149
  readonly parentTrack: any;
149
150
  renderProps(): any;
@@ -178,7 +179,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
178
179
  readonly featureDensityStatsReady: boolean;
179
180
  readonly maxAllowableBytes: number;
180
181
  } & {
181
- afterAttach(): void;
182
+ afterAttach(): void; /**
183
+ * #getter
184
+ */
182
185
  } & {
183
186
  setCurrStatsBpPerPx(n: number): void;
184
187
  setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
@@ -225,6 +228,16 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
225
228
  } & {
226
229
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
227
230
  afterAttach(): void;
231
+ } & {
232
+ /**
233
+ * #property
234
+ */
235
+ rowHeight: number;
236
+ } & {
237
+ /**
238
+ * #getter
239
+ */
240
+ readonly sequenceHeight: number;
228
241
  } & {
229
242
  /**
230
243
  * #method
@@ -292,9 +305,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
292
305
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
293
306
  }, {
294
307
  renderInProgress: AbortController | undefined;
295
- /**
296
- * #method
297
- */
298
308
  filled: boolean;
299
309
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
300
310
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -304,8 +314,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
304
314
  message: string | undefined;
305
315
  maxHeightReached: boolean;
306
316
  ReactComponent: ({ model, }: {
307
- model: any;
308
- }) => any;
317
+ model: {
318
+ error?: unknown;
319
+ reload: () => void;
320
+ message: import("react").ReactNode;
321
+ filled?: boolean | undefined;
322
+ status?: string | undefined;
323
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
324
+ };
325
+ }) => import("react").JSX.Element | undefined;
309
326
  renderProps: any;
310
327
  } & {
311
328
  doReload(): void;
@@ -338,7 +355,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
338
355
  height: {
339
356
  type: string;
340
357
  defaultValue: number;
341
- description: string;
358
+ description: string; /**
359
+ * #property
360
+ */
342
361
  };
343
362
  mouseover: {
344
363
  type: string;
package/esm/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -30,6 +30,26 @@ export function modelFactory(configSchema) {
30
30
  * #property
31
31
  */
32
32
  showTranslation: true,
33
+ }))
34
+ .volatile(() => ({
35
+ /**
36
+ * #property
37
+ */
38
+ rowHeight: 15,
39
+ }))
40
+ .views(self => ({
41
+ /**
42
+ * #getter
43
+ */
44
+ get sequenceHeight() {
45
+ const { showTranslation, showReverse, showForward } = self;
46
+ const r1 = showReverse && showTranslation ? self.rowHeight * 3 : 0;
47
+ const r2 = showForward && showTranslation ? self.rowHeight * 3 : 0;
48
+ const t = r1 + r2;
49
+ const r = showReverse ? self.rowHeight : 0;
50
+ const s = showForward ? self.rowHeight : 0;
51
+ return t + r + s;
52
+ },
33
53
  }))
34
54
  .views(self => {
35
55
  const { renderProps: superRenderProps } = self;
@@ -38,7 +58,7 @@ export function modelFactory(configSchema) {
38
58
  * #method
39
59
  */
40
60
  renderProps() {
41
- const { showForward, rpcDriverName, showReverse, showTranslation } = self;
61
+ const { showForward, rpcDriverName, showReverse, showTranslation, rowHeight, sequenceHeight, } = self;
42
62
  return {
43
63
  ...superRenderProps(),
44
64
  config: self.configuration.renderer,
@@ -46,6 +66,8 @@ export function modelFactory(configSchema) {
46
66
  showForward,
47
67
  showReverse,
48
68
  showTranslation,
69
+ rowHeight,
70
+ sequenceHeight,
49
71
  };
50
72
  },
51
73
  };
@@ -91,13 +113,7 @@ export function modelFactory(configSchema) {
91
113
  self.setHeight(50);
92
114
  }
93
115
  else {
94
- const { showTranslation, showReverse, showForward } = self;
95
- const r1 = showReverse && showTranslation ? 60 : 0;
96
- const r2 = showForward && showTranslation ? 60 : 0;
97
- const t = r1 + r2;
98
- const r = showReverse ? 20 : 0;
99
- const s = showForward ? 20 : 0;
100
- self.setHeight(t + r + s);
116
+ self.setHeight(self.sequenceHeight);
101
117
  }
102
118
  }));
103
119
  },
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "2.10.2",
3
+ "version": "2.10.3",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -57,5 +57,5 @@
57
57
  "distModule": "esm/index.js",
58
58
  "srcModule": "src/index.ts",
59
59
  "module": "esm/index.js",
60
- "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
60
+ "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
61
61
  }